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Has anyone ever wondered what would've happened had "A Canterlot Wedding" given Rarity top billing. Here's the most likely answer. Just be grateful it was Twilight who had the older brother from Celestia's plot.
Notably, Rarity was absent from Luna Eclipsed. So, what happened? Was she just tired and went to bed for the evening? Was it as Lauren Faust said and that her scene was cut due to time constraints and redundancy? Or...
At least two of the many, many alternate endings to the infamous Cupcakes has the events all just being a fanfic written by one of the Mane Cast. Another has it all being just an Alfred Hitchcock play.
Ponies Play D&D. The initial story of Applejack playing her first Dungeons & Dragons game after everyone else has gotten addicted to it is funny enough, but then it hits a whole new level when the CMC find the gamebooks and each of the mane cast takes a turn as DM.
The Worst Bakers In Equestria has plenty, but one that combines this with awesome is Trixie's semi-semi-final baking attempt. The sheer over-the-topness of it as Trixie's personal Doom Magnet levels of bad luck actually animates her baking attempt into a ravening dough-monster, forcing her to duel it into submission. Commentators Spike and Pinkie Pie are at a complete loss of words over it, and by the end of it, the entire audience in perfect synchronization reset their mouths after they had been dropped in awe.
The Elements of Gaming: In chapter 8, Rainbow Dash and Applejack go into rivalry-mode while playing Burnout, only for them and everyone else in the race to be thoroughly trounced by an unknown (the others being easily identified as Hoops, Score, Dumbbell, and Scootaloo) player with the screen-name of Muffin_Master (you can probably see where this is going). Muffin_Master, naturally, turns out to be none other than Ditzy "Derpy Hooves" Doo.
Also from that chapter: Rarity's reaction to Scootaloo being one of the players, because Scootaloo had told her that she and Sweetie Belle were going to go study.
Rarity: Oh Girls... Do go on without me, would you please? I do believe I've got... problems to take care of. Three very hyperactive problems.
Twilight becoming angry because Pinkie bluescreened the computer from spamming too many Nod militants. Let's just say that her enraged Rapidash form wasn't a good idea to use in the library.
You could probably guess how annoying it was to hear "Fighters arm up!" as she spam builded them.
Along with that: Rarity annihilating the AI opponent when they attacked her perfectly constructed base.
Or Dash facing down 2 hard AIs.
Or in the first chapter, the mane cast having problems with Halo: Reach's legendary difficulty.
Like Twilight starting to swear like Princess Clara when she kept getting killed at a certain point.
In Chapter 2, Twilight and company get to test out Gears of War. She expects Rainbow Dash and Applejack to love it, and they do... until Pinkie starts playing, and gleefully uses the chainsaw bayonet on an enemy, which makes everypony else lose their lunch.
Then comes chapter 3.5, in which Twilight gets hooked on Tetris and plays so well that Pinkie literally shits a pile of bricks while watching her.
The Birds and the Bees, with the mane six each giving their own version of The Talk to the CMC. The punchline everyone's undoubtedly waiting for when they finally ask Pinkie Pie is completely worth the buildup.
Like Fine Wine may be highly explicit material, but as you'd expect from the author of Romance Reports, it has a few funny moments as well, one of the best being Rarity's reaction upon seeing Spike's Exotic Equipment for the first time.
Pinkie Pie Discovers Coffee The real laughs come from the fact that it's not Pinkie Pie that goes nuts after drinking coffee, but Twilight Sparkle.
Suddenly, Twilight became a living ball of energy, exploding up into the air and launching straight for the Cakes. They were taken off guard as she tackled them to the ground, her pupils shrinking as she became the horror they were afraid of.
The fanfic Estrus has a lengthy conversation between five of the Mane Six over how they should break the news to Twilight about the symptoms of heat she's feeling. note She's actually already figured it out - she just hadn't heard it referred to as "in heat" before, only knowing it as "estrous cycle". It contains a lot of hilarious details of how each of them learned about the facts of life and how each chooses to deal with the symptoms. Applejack ends up calling "Too Much Information" on the conversation when Pinkie Pie and Fluttershy start comparing vibrators.
The same author's Fluffershy, in which Hilarity Ensues after Pinkie finds a porn DVD in Mr. Cake's collection with what she recognises as Fluttershy's butt on the cover. The rest of the Mane Six find out about it - except Rainbow, who already had three copies on various formats - and when Fluttershy walks in on them watching her scene, she attempts to commit seppukuwith Angel's carrot.
Strong Bad: "Wait, you're not Marzipan! Who is this? You mean there's actually someone else who has an answering machine? Well that's a load of crap. Although you sound pretty hot. Mmm yeah, hey there, baby. Wanna go out with the one and only Strong Bad? I mean, it's not like you're a purple horse or anything."
Homestar Runner: "Whoa, Marzipan! What happened to your voice? I mean, you sound different. Like, did you turn yourself into a talking, purple unicorn or something? Because that's great! I always wanted a unicorn girlfriend for me to break up with!"
Peachy: It worked for us. Twenty-five years since he first stole me away from that low-life mugger I was with, and I haven't looked back.
Andrew Joshua Talon's Hands has many moments of humor in it, but this tropers favorite is his SI's reaction to New Fluttershy and getting kicked out of her house after she came back from Iron Will's Seminar. He immediatly heads to Twilight's house and the first thing he says upon Twilight opening the door: ""Fluttershy has been possessed and we need to save her immortal soul."
Imagine hearing the words "Even if you are a twisted, bondage-loving masochistic bisexual nymphomaniac, we still love you." Now imagine hearing Fluttershy be the one who says that like she did here. 
For some Original Flavour fantasy-slapstick, the story Study Break, in which Hilarity Ensues after Twilight unwittingly eats an enchanted apple from a tree in the Canterlot palace grounds, which causes random magical effects when she sneezes, always at the worst possible time.
Fluttershy: A pony wouldn't just flop after being slashed like that! There would be at least some spasm or other reflex action! And the blood spray? Way too even, like someone was spraying it with a hose. It's like Starlight didn't even have a heartbeat, and the viscosity is just far too low for aortic blood. Has the director ever seen a severed aorta? And while I'm on the subject, how can I expect to take this seriously when there's no evidence of trauma to her vital organs with a cut that deep? Honestly, any pony with a basic understanding of pony anatomy could see how fake this is!
Also, Rarity's "threats" to Rainbow Dash. Like when Dash threatens to start the "chimicherrychanga" rant:
Rarity: You finish that word, punk, and I will style your hair. I will make you beautiful! There will be curling irons involved. When I am done, I am going to wash that mane of yours, and condition it. It will be silky-smooth for weeks. Do I make myself clear?
Or when Dash tries to join Pinkie in mentioning Rarity's embarrassing moments by bringing up the Sonic Rainboom incident:
Rarity: By Fancy's Pants, if you make a lame pun about me falling for you, head over hooves or otherwise, I will take you shoe shopping! And then I'll get you a nice, bright, fancy dress! With sequins. Are we clear?!
Rainbow Dash (terrified): C-Crystal.
Before Fluttershy's rant, Twilight comments that Rarity apparently likes to write about Blueblood dying horribly; one particularly gruesome story involved a cider mug and a broom.
In chapter eight of My Little Mommies, Pinkie Pie is telling the Cakes about how a magic mirror created a baby by combining traits from her and Fluttershy. To Fluttershy's surprise, the Cakes pretty much accept this immediately and congratulate Pinkie.
What does Pinkie Pie leave behind for Twilight and Blueblood at the end of Royal Courtin' found here? A condom
And it turns out to be broken
This fic about Shining learning a surprising fact about his wife. How her name is actually spelled. Bonus points for what it does with the premise.
This fic features Fluttershy competing in the World Quiet Game Championships. Not only are said Championships played as Serious Business to the point thousands of fans are in attendance and Princess Celestia is the judge (much to Twilight and Rarity's shock), Fluttershy's opponents are Nightmare Moon (actually Luna in disguise to try and throw off her competition), Shy Sparrow (a dead unicorn skeleton who's Last Request was for his corpse to compete), and Angel. Rarity also enters the amateur competition and loses in a couple seconds.
Don't let the fanfic Mommy Nearest fool you with how sad it starts. Yes, it's about Rainbow Dash having a horrible accident and having brain damage, but it ends on the hilarious note of Rainbow Dash being revealed as Princess Celestia's illegitimate daughter, specifically with an earth pony. And I am going to warn you right now, if you've ruined that hilarious twist, there's one more so hilarious that I dare not put it in spoilers, it's so ridiculous.
In Halcyon Hearts, Shining Armor learns from Celestia that Twilight has finally gotten a boyfriend - a recently-paroled convict named Blaze. The story cuts to Twilight and her boyfriend enjoying their first proper date, and then towards the end of the scene:
Twilight: Do you hear something?
Blaze: No, why?
Twilight: I could have sworn I heard somepony calling my name just now...it sounded angry.
Hail to the King is just wall to wall hilarity, as a recently deceased human's soul gets diverted to inhabit the body of the recently defeated King Sombra. Everypony assumes that Sombra is still crazy, but instead of just Ax-Crazy, they think he's out of his mind.. And he isn't helping his case, particularly when trying to explain what he really is.
Shining Armor: Then how come I've never met one? We should be drowning in a sea of humans by now.
Cadence: Because we're just figments of his imagination, remember? So that's where his mind is right now. He's a hyper-evolved, futuristic, thunder-monkey.
In Tails, Sweetie Belle and the other CMC experiment with her magic by removing their sisters' tails and switching them around, intending to switch them back before they wake up. This doesn't go well. The best part? It gets Sweetie Belle her cutie mark!
In Daleks Have No Concept Of Friendship, a dying Dalek, having found itself on Equestria by Celestia herself, is transformed into a pony. But just because it's a pony, doesn't mean it's not a Dalek...
In The King Is Dead, Long Live The Emperor, the author gives an explanation of how time travel and alternate universes work, and at one point gives an example of several possible ways King Sombra could have been stopped. One of those ways involved being banished to the realm of shadows by a wise-cracking mule armed with a magic kazoo. Cue several requests from the fandom asking for the full story. The author's response? Essentially, that the world was not ready, and that if he ever posted it, the internet would explode. Twice.
In the same chapter, he explains how alternate universes exist, and I quote, because scientists and wizards everywhere will not stop poking the fabric of reality with the equivalent of a sharp stick, just to see what happens. And that, due to being unable to tell the difference between a disintegration spell and a one-way time travel spell, some alternate universes exist only because somepony was too lazy to take out the trash.
There's also It is said that love conquers all. This is quite true: The magical energy of love is capable of ignoring all manner of factors, including time and space. Love laughs at mere distance, and farts in the general direction of such a meager concept as years, or even decades. That is simply how love rolls... and if you try to question it, love will mare-slap you for talking back to it.
Stealing the Deed has Twilight and Spike coming home to find Trixie raiding the fridge after smashing the (unlocked) front door, and dances between Trixie using darkly humorousInsane Troll Logic to prove that she now owns Twilight's home, to her both confirming and very badly denying a Yandere streak for Twilight. At one point, after arguing with a magistrate, Trixie finds herself in jail, and Twilight offers to get her out, if only to save the sanity of anyone having to listen to her at trial. Only for Trixie's yandereness to flare up once again and cause Twilight to wonder if Rarity needs any help crying in the shower.
Celestia considered going after Twilight and trying to explain that a Class 5 magical detonation was not going to solve her problems, but considering that it was Chrysalis on the receiving end, she decided that it would be much more entertaining for her to simply sit back and enjoy the show.
As Chrysalis turned into nothing more than a black speck above the clouds, Twilight realized she had forgotten to account for variations in the gravitational field of Equus in her orbital mechanics, and that Chrysalis would likely miss the moon by several miles.
Oh well, that wasn't important.
And, in the wrap-up:
Celestia: And furthermore, giant explosions are not how you solve problems.
It had been a good few thousand years since Celestia had taken up the throne. She had been required to speak that line to a disconcerting number of her students. Her students, being exceptionally smart unicorns, often came up with memorable objections to not using large explosions to solve problems, including "but isn't the sun basically a giant perpetual explosion?" and "but explosions are more fun!" This, sadly, did nothing to prepare her for Twilight's answer.
Twilight Sparkle: That's not true! The inverse explosion law states that, as the size of an explosion increases, the number of problems it is incapable of solving quickly approaches zero!
The best part about this line was that it was inspired by a comment someone had made on the story. The author liked it so much he incorporated into the epilogue.
Adagio Dazzle: Why, Sunset! I’m hurt! And after we hit it off so well yesterday. Sunset Shimmer: Right, sorry. Just having a bad day here… and it’s barely started even. I guess I shouldn’t take it out on you and— Sonata Dusk: Hit it off? I thought you said we might have to do something about that 'stupid preppy Shimmer girl' if we ever want our plans to succeed! Adagio: *facepalm* Sonata: And the after that pink-haired girl made a song about wearing pink, you said we definitely had to do something about her and her friends! Adagio: UGH! Why do we even let you outside?!? Sonata: Because you have no choice now that I figured out how locks work?
Past Sins has an in-progress MST of the original edit of the story, which can be found here. While it's only gotten the prologue and the first three chapters finished, with Chapters 4 to 7 currently being worked on, it's shaping up to be hilarious.
During the run-down of the two characters, Starscream's appearance in the execrable Kiss Players manga is mentioned, where he possessed a cybernetic schoolgirl while she was in the bathroom, then forgot to pull her underwear up.
Boomstick: Props to you, Japan. I did not see that one coming.
Special mention to Boomstick slowly being bought over to Rainbow Dash's side.
Boomstick: This is a pony. A baby horse girl toy. Why is it so awesome!?
This interpretation of how the season 2 finale could have gone.
Bronies React is full of them, but one good one is in the first episode, where they're reacting to the Teens React to My Little Pony: Friendship is Magic episode. In the episode the bronies are reacting to, one of the teens is asked why they think they're being shown this, and responds with "Maybe you think I'm on the other side of the street, and I'm not?" Cue Flat "What." stares and gestures from each of the bronies. Even Solrac / Yaplap is left speechless.
Teen: Get a life! I mean, come on! Joshscorcher: ... said the teenager to the Marine.
Teen (different one): These guys probably have way too much time on their hands. Joshscorcher: (laughs hysterically until he's out of breath) *beat* You're serious.
Teen: Maybe you think I'm on the other side of the street, and I'm not? Joshscorcher: Ya know, you can actually say the words 'homosexual' or 'gay'. It's not going to make you burst into flames.
Teen (yet another one, with a ridiculous hairdo): If you're a guy and you watch My Little Pony, you technically shouldn't be allowed to be called a man. KingHarald: When your head looks like a Justin Bieber ad, you don't get to say who is and who isn't a man.
Teen (same one as above): You stop being bronies, or I'm going to whack you with your silly little ponies.
BlackGryph0n:note BlackGryph0n has been through Navy frogman training (even if he failed to graduate due to injuries), is in top physical condition, and outweighs the kid in question by at least 50 lbs.Oh, that was so clever. I am so intimidated by that guy. Did you see his arms? They're like fingers.
Joshscorcher: (riffing on the other guy's voice) You'd better believe what I believe or else I will hurt you! (stops) This guy is nineteen! An adult! *beat* He's not being a very good role model.
Pinkie Pie:note for the full text of Pinkie's rant by the mailbox, consult the Insane Troll Logic entry in the episode recap ... and it will be all. my. FAULT! Joshscorcher: You know, that's kinda how my mom was when I was at boot camp.
Spitfire: Why don't you two go hit the mess hall early? Joshscorcher: ...SAID NO DRILL INSTRUCTOR EVER!
And actual insightful commentary from their own experiences... complete with deadpan snark:
(Lightning Dust gets her insignia ripped off) Joshscorcher: Now, a lot of people seem to have complained that that punishment was too excessive. Well, in real life that would have been getting off easy. I mean... due to your own recklessness, you endangered your life and the lives of the people around you? (A caption pops up on the screen saying "PEOPLE HAVE BEEN SENT TO THE BRIG FOR LESS"). Yeah, she got off easy just being kicked out. (on-screen, Spitfire is taking Lightning Dust's badge and slapping it onto Rainbow Dash's chest — pin first) BlackGryph0n: ... am I the only one who thought that looked really painful?
BlackGryph0n: Obviously it wasn't nearly as tense as actual military training, but they couldn't really do that in a children's show. *beat* In fact, they probably shouldn't do that in an adult show.
But the most noteworthy part is Jake The Army Guy (who is a drill instructor in real life) doing his own completely over the top Drill Sergeant Nasty routine, synchronized to the action on-screen. A sample follows:
Lightning Dust (in her intro scene, mouthing off to Spitfire): Try me, ma'am! (the camera does a brief cut to several of the commentators, showing them all staring at their screens in literal jaw-dropping horror, with BlackGryph0n flatly noting that in a realistic boot camp Lightning Dust would be a dead mare walking) Jake:PRIVATE DUST! (puts his face two inches away from the camera) Let me ask you a question, Private, and be honest, because I'm a little confused here. What in the wide wide world of sweet FUCK makes you think YOU CAN MOUTH OFF TO YOUR COMMANDING OFFICER LIKE THAT?!? Do you want to die? THEN WHY DON'T YOU DO THE WORLD A FAVOR AND GO PRACTICE HOW TO SUCK-START YOUR M-16! *Beat* Are you eyeballing me, Private? YOU BETTER NOT BE! YOU ARE AT THE POSITION OF ATTENTION! YOUR HEAD AND EYES ARE STRAIGHT FORWARD, YOU POSTER CHILD FOR BACK-ALLEY ABORTIONS! YOU- *incoherent noises* Private, you have exactly five seconds to stop eyeball-fuckin' me, or so help me Celestia I'M GONNA RIP YOUR LUNA-DAMNED THROAT OUT AND MAKE SWEET SWEET LOVE TO THE HOLE!
By the time the video is finished, Jake has blasphemed in the name of every alicorn then extant in Equestria. Some of them repeatedly.
Celestia: Oh my God, are you nerds really getting worked up about this? You guys need to learn how to relax. You know I've got a strat. Luna: Celestia, please. We need something stronger. Cadance: What are you talking about? What strat? Celestia: Luna, the 'Let Twilight Handle That Shit' technique is tried and tested. Cadance: Ooh! Yeah, that sounds great. Let's do that. Luna: That is not a viable long-term strategy! Celestia: Yeah, because doing what works every time is SO CRAZY. Seriously, let's just give her our magic or something. Game of Thrones is on.
Celestia: Oh yeah. You see, my strat's full name is the 'Let Twilight Handle That Shit And Totally Fuck With Her' technique. Four years ago, when Nightmare Moon was coming back, I told her she had to go live in a public library, as a joke. She's still there. She thinks it's awesome. Since then, fucking with Twilight has been a time-honored tradition. Cadance: I support this. I support this so hard. So, we give her all our magic, and then... ooh, I know! What if we tell her that she can't tell any of her friends? Ehhh, I guess that's kinda weak. Celestia: No no, I love it! That'll mess her up. Man, we don't hang out often enough. You're pretty cool. Luna: Oh for crying out loud! Why don't you just banish her to the moon if you like her so much? *storms out* Celestia: Man, are you still not over that?